In this paper we present a multi-modal security-transportation model to allocate security resources within a chemical supply chain which is characterized by the use of different transport modes, each having their own security features. We consider security-related risks so as to take measures against terrorist acts which could target critical transportation systems. The idea of addressing security-related issues, by supporting decisions for preventing or mitigating intentional acts on transportation infrastructure, has gained attention in academic research only recently. The decision model presented in this paper is based on game theory and it can be employed to organize intelligence capabilities aimed at securing chemical supply chains. It enables detection and warning against impending attacks on transportation infrastructures and the subsequent adoption of security countermeasures. This is of extreme importance for preventing terrorist attacks and for avoiding (possibly huge) human and economic losses. In our work we also provide data sources and numerical simulations by applying the proposed model to a illustrative multi-modal chemical supply chain.